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Two things:
(1) Trials should last as long as the neural activity lasts for the stimuli in the study;
(2) You should always jitter the ISI.

As to your second question, you can not ensure that all subjects will not have any residual pain in the experiment. You want to minimize this from happening. This can be done with longer ISIs.

To optimize the design, use optseq2. To use the program you need to know how long the neural activity related to pain lasts as the program needs to know about your stimuli to select the best model.

Best Regards, Donald McLaren
=================
D.G. McLaren, Ph.D.
Research Fellow, Department of Neurology, Massachusetts General Hospital and
Harvard Medical School
Postdoctoral Research Fellow, GRECC, Bedford VA
Website: http://www.martinos.org/~mclaren
Office: (773) 406-2464
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On Sun, Jun 22, 2014 at 10:41 PM, Andy Yeung <[log in to unmask]> wrote:
Dear all,

I've read that jittering the ISI between multiple stimuli entities can increase design efficiency by reducing correlation of regressors of the stimuli. (Handbook of functional MRI data analysis by RA Poldrack et al.)

What if my stimuli may have carry-over effect which need certain period of time to stop that. For example (just saying), if I gave different pain (or taste) stimuli to subjects who need a minimal 3 seconds to feel no more pain. Should I employ ON-OFF block with fixed OFF at 3 s to maximize the number of repetition, or should I jitter ISI by assigning OFF from 3 s to something like 6 s?

Second question is, considering LTI property of HRF, do I have to ensure subjects feel no pain (caused by previous pain stimulus) at the start of every pain presentation?

How can I maximize the design efficiency? Thanks for your time and consideration.

Best,
Andy